For certain applications, like hematological cancers, you might want to make sure that certain sets of genes either do not get marked as highly variable genes or they do (as you might want to make sure that they don't/do influence downstream processes of clustering). There should be an option then on the HVG method that receives a file with a list of genes to either make sure they are marked as HGVs or they are not (could be passed as two separate set of genes in case you want to do both). Then, after HGVs are marked, then those genes are either set as True or False on the obs column for HGVs.
For certain applications, like hematological cancers, you might want to make sure that certain sets of genes either do not get marked as highly variable genes or they do (as you might want to make sure that they don't/do influence downstream processes of clustering). There should be an option then on the HVG method that receives a file with a list of genes to either make sure they are marked as HGVs or they are not (could be passed as two separate set of genes in case you want to do both). Then, after HGVs are marked, then those genes are either set as True or False on the obs column for HGVs.